Hi,
I have been recently dealing with the Personal Genomes Project, and trying to work with the data. I downloaded the raw data for an individual's whole genome.
The main concern is the format of the data. Complete Genomics frees the genomes of the individuals in its own format; a format called masterVar which looks like this:
#ASSEMBLY_ID GS000014558-ASM
#COSMIC COSMIC v48
#DBSNP_BUILD dbSNP build 132
#GENOME_REFERENCE NCBI build 37
#SAMPLE GS01669-DNA_D02
#GENERATED_BY cgatools
#GENERATED_AT 2012-Sep-28 19:43:38.251270
#SOFTWARE_VERSION 2.0.4.14
#FORMAT_VERSION 2.0
#GENERATED_BY dbsnptool
#TYPE VAR-ANNOTATION
>locus ploidy allele chromosome begin end varType reference alleleSeq varScoreVAF varScoreEAF varQuality hapLink xRef
17 2 all chr1 11365 11370 ref = =
302 2 1 chr1 21579 21580 snp C T 123 123 VQHIGH dbsnp.83:rs526642
302 2 2 chr1 21579 21580 snp C T 153 153 VQHIGH dbsnp.83:rs526642
They provide some tools to work on it and I tried to convert to vcf with this tool, but what I get is some kind of funny vcf, with duplicated entries and inconsistent information.
Has anyone dealt with it before?
Thanks in advance!
P.
1 answer
You could use the CGAtools and use the following command, I left out the CGA_CEHQ and CGA_CEGL field
/software/cgatools/current/bin/cgatools mkvcf --beta --reference build36.crr \
--source-names masterVar \
--genome-root $root \
--master-var <(bzcat $masterVar) \
--field-names GT,PS,NS,AN,AC,AF,SS,FT,CGA_XR,CGA_ALTCALLS,CGA_FI,GQ,HQ,EHQ,GL,DP,AD,CGA_RDP,CGA_ODP,CGA_OAD,CGA_ORDP,CGA_PFAM,CGA_MIRB,CGA_RPT,CGA_SDO,CGA_SOMC,CGA_SOMR,CGA_SOMS,CGA_SOMF,GT,CGA_GP,CGA_NP,CGA_CP,CGA_PS,CGA_CT,CGA_TS,CGA_CL,CGA_LS,CGA_LAFS,CGA_LLAFS,CGA_ULAFS,CGA_SCL,CGA_SLS,CGA_LAFP,CGA_LLAFP,CGA_ULAFP,GT,FT,CGA_IS,CGA_IDC,CGA_IDCL,CGA_IDCR,CGA_RDC,CGA_NBET,CGA_ETS,CGA_KES,GT,FT,CGA_BF,CGA_MEDEL,MATEID,SVTYPE,CGA_BNDG,CGA_BNDGO,CGA_BNDMPC,CGA_BNDPOS,CGA_BNDDEF,CGA_BNDP
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written
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ash.avalon •
This pretty much worked for me - however I had to first convert my genome.fa reference into the CRR format using another cgatool:
$cgatools fasta2crr --input build36.fa.bz2 --output build36.crr
see docs http://cgatools.sourceforge.net/docs/1.4.0/cgatools-install.pdf
Also for those not familiar with linux you need to assign your filename to masterVar variable (masterVar=my_file.tzv.bz2) for the <(bzcat $masterVar) part to work ( Note: not to be confused with the masterVar string in --source-names masterVar that tells the program the conversion type)
Also --genome-root $root was complaining so I left that parameter out (which seems to be OK if you also leave out the CGA_CEHQ and CGA_CEGL as suggested above).
In the process of converting 380 file now and seems to be producing sensible VCF files
(For the record the masterVar2VCF_rev1_ShanYang.zip converter on the complete genomics website did not work for me either. producing corrupt files)
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written
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kenny.bryan •
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Hi, I'm dealing with the same issue. Did you figure out any way to convert Complete Genomics to vcf or to plink ped format without bugs?
Thank you.
Hi, Unfortunately I was not able to make it work and quited by now. As said, I tried different conversion tools, but all returned a very weird file with clear errors compared to original. I am really surprised that no further information on this issue explaining the thing a bit more could be found... Anyway, if you get to know anything else, let me know about it, Best,